[Debian-med-packaging] Bug#853568: No idea how to fix abs arguments in nanopolish

[Walter Landry]

Andreas Tille <andreas at an3as.eu> wrote:
> Hi,
> 
> to fix bug #853568 I tried a patch (gcc-7.patch) to fix abs() arguments
> in nanopolish[1] but I have no idea how to deal with this:
> 
> ...
> g++ -o src/hmm/nanopolish_pore_model_set.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate-t
> src/common/nanopolish_variant.cpp: In function 'std::vector<Variant> extract_variants(const string&, const string&)':
> src/common/nanopolish_variant.cpp:32:69: error: call of overloaded 'abs(std::__cxx11::basic_string<char>::size_type)' is ambiguous
>      size_t difference = std::abs(reference.size() - haplotype.size());

The result of subtracting two size_t's is still a size_t, which is
unsigned.  So you need to cast it to a signed type.  The correct type
is ptrdiff_t.

  http://en.cppreference.com/w/cpp/types/ptrdiff_t

The line then becomes

  size_t difference = std::abs(static_cast<ptrdiff_t>(reference.size() - haplotype.size()));

Or you could do it in two lines

  ptrdiff_t diff_signed (reference.size() - haplotype.size());
  size_t difference = std::abs(diff_signed);

Cheers,
Walter Landry